7-138205280-T-G

Variant names:

• chr7-138205280-T-G
• rs11761248

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.279 in 151,996 control chromosomes in the GnomAD database, including 6,514 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42364 AN: 151878 Hom.: 6516 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.266

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42374 AN: 151996 Hom.: 6514 Cov.: 32 AF XY: 0.282 AC XY: 20974 AN XY: 74288

African (AFR) AF: 0.181 AC: 7520 AN: 41472

American (AMR) AF: 0.254 AC: 3874 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1146 AN: 3462

East Asian (EAS) AF: 0.168 AC: 868 AN: 5168

South Asian (SAS) AF: 0.280 AC: 1345 AN: 4800

European-Finnish (FIN) AF: 0.429 AC: 4514 AN: 10532

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22104 AN: 67982

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.263 Hom.: 3310

Bravo AF: 0.257

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11761248; hg19: chr7-137890026;